相关实验视频

Updated: Jan 9, 2026

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

在氨基酸模拟的联合原子模型中开发外空间静电电位适配电荷

Fengyu Li¹, Yuwei Zhang², Fei Xia³

¹Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Sciences, Research Center for Chemical Theory, Departments of Chemistry, Fudan University, Shanghai 200433, China.

Journal of chemical theory and computation

|December 1, 2025

概括

一种新的外空间静电电位 (SS-ESP) 方法准确地捕捉了粗粒度 (CG) 模型中的静电相互作用. 这种方法使得氨基酸的新侧链减少CG (SRCG) 模型成为可能,改善了蛋白质模拟.

科学领域:

计算化学是一种计算化学.
生物分子建模模型
统计力学就是统计力学.

背景情况:

准确的静电相互作用对于生物分子模拟中的粗粒度 (CG) 模型至关重要.
在CG模型中推导部分电荷的现有方法可能缺乏精度.
全原子 (AA) 模型为开发CG力场提供了高可靠性参考.

研究的目的:

开发一种新的外空间静电电位 (SS-ESP) 方法,用于在CG模型中推导部分电荷.
根据SS-ESP方法,为氨基酸引入新的侧链减少CG (SRCG) 模型.
通过AA模拟来验证SS-ESP方法和SRCG模型的准确性.

主要方法:

开发了外空间静电电位 (SS-ESP) 方法,以适应AA模型中的静电电位 (ESP).
通过四种不同的方法与AA氨基酸模型比较CG电荷的ESP和电二极子时刻.
使用自下而上的策略参数化了SRCG力场:从AA继承了粘接参数,通过SS-ESP获得了CG电荷,并将Lennard-Jones参数与范德瓦尔斯电位相匹配.

主要成果:

与AA模型相比,SS-ESP方法准确地复制ESP和双极时刻.
使用SS-ESP电荷进行参数化的SRCG模型显示了对二和三的AA模拟的一致性.
SRCG力场准确地预测了溶解自由能量,并保持了蛋白质二次结构的稳定性.

结论:

SS-ESP电荷配合方法为CG粒子中精确的静电相互作用提供了一个强大的框架.
开发的SRCG模型为蛋白质模拟提供了氨基酸的可靠和准确的表示.
这项工作推进了蛋白质CG模型的自下而上的开发,并改进了静电描述.

更多相关视频

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Published on: October 21, 2018

相关概念视频

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Electronic Structure of Atoms

Electronic Structure of Atoms

An atom comprises protons and neutrons, which are contained inside the dense, central core called the nucleus, with electrons present around the nucleus. Taking into account the wave–particle duality of electrons and the uncertainty in position around the nucleus, quantum mechanics provides a more accurate model for the atomic structure. It describes atomic orbitals as the regions around the nucleus where electrons of discrete energy exist, characterized by four quantum...

Atomic Radii and Effective Nuclear Charge

Atomic Radii and Effective Nuclear Charge

The elements in groups of the periodic table exhibit similar chemical behavior. This similarity occurs because the members of a group have the same number and distribution of electrons in their valence shells.

VSEPR Theory

VSEPR Theory

Valence shell electron-pair repulsion theory (VSEPR theory) enables us to predict the molecular structure around a central atom from an examination of the number of bonds and lone electron pairs in its Lewis structure. The VSEPR model assumes that electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between these electron pairs by maximizing the distance between them. The electrons in the valence shell of a central atom form either bonding...

The Energies of Atomic Orbitals

The Energies of Atomic Orbitals

In an atom, the negatively charged electrons are attracted to the positively charged nucleus. In a multielectron atom, electron-electron repulsions are also observed. The attractive and repulsive forces are dependent on the distance between the particles, as well as the sign and magnitude of the charges on the individual particles. When the charges on the particles are opposite, they attract each other. If both particles have the same charge, they repel each other.

The Quantum-Mechanical Model of an Atom

The Quantum-Mechanical Model of an Atom

Shortly after de Broglie published his ideas that the electron in a hydrogen atom could be better thought of as being a circular standing wave instead of a particle moving in quantized circular orbits, Erwin Schrödinger extended de Broglie’s work by deriving what is now known as the Schrödinger equation. When Schrödinger applied his equation to hydrogen-like atoms, he was able to reproduce Bohr’s expression for the energy and, thus, the Rydberg formula governing hydrogen spectra.